Ignore:
Timestamp:
Apr 29, 2010, 1:55:21 PM (16 years ago)
Author:
Tillmann Crueger <crueger@…>
Children:
070651, 5d1a94
Parents:
90c4460 (diff), 32842d8 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
Message:

Merge branch 'VectorRefactoring' into StructureRefactoring

Conflicts:

molecuilder/src/Legacy/oldmenu.cpp
molecuilder/src/Makefile.am
molecuilder/src/analysis_correlation.cpp
molecuilder/src/boundary.cpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/ellipsoid.cpp
molecuilder/src/linkedcell.cpp
molecuilder/src/molecule.cpp
molecuilder/src/molecule_fragmentation.cpp
molecuilder/src/molecule_geometry.cpp
molecuilder/src/molecule_graph.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/tesselation.cpp
molecuilder/src/tesselationhelpers.cpp
molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp
molecuilder/src/unittests/bondgraphunittest.cpp
molecuilder/src/vector.cpp
molecuilder/src/vector.hpp

File:
1 edited

Legend:

Unmodified
Added
Removed

  • molecuilder/src/config.cpp

    r90c4460 r0d111b  
    742742              neues = AtomList[i][j];
    743743            status = (status &&
    744                     ParseForParameter(verbose,FileBuffer, keyword, 0, 1, 1, double_type, &neues->x.x[0], 1, (repetition == 0) ? critical : optional) &&
    745                     ParseForParameter(verbose,FileBuffer, keyword, 0, 2, 1, double_type, &neues->x.x[1], 1, (repetition == 0) ? critical : optional) &&
    746                     ParseForParameter(verbose,FileBuffer, keyword, 0, 3, 1, double_type, &neues->x.x[2], 1, (repetition == 0) ? critical : optional) &&
     744                    ParseForParameter(verbose,FileBuffer, keyword, 0, 1, 1, double_type, &neues->x[0], 1, (repetition == 0) ? critical : optional) &&
     745                    ParseForParameter(verbose,FileBuffer, keyword, 0, 2, 1, double_type, &neues->x[1], 1, (repetition == 0) ? critical : optional) &&
     746                    ParseForParameter(verbose,FileBuffer, keyword, 0, 3, 1, double_type, &neues->x[2], 1, (repetition == 0) ? critical : optional) &&
    747747                    ParseForParameter(verbose,FileBuffer, keyword, 0, 4, 1, int_type, &neues->FixedIon, 1, (repetition == 0) ? critical : optional));
    748748            if (!status) break;
    … …  
    758758            // put into trajectories list
    759759            for (int d=0;d<NDIM;d++)
    760               neues->Trajectory.R.at(repetition).x[d] = neues->x.x[d];
     760              neues->Trajectory.R.at(repetition)[d] = neues->x[d];
    761761
    762762            // parse velocities if present
    763             if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 5, 1, double_type, &neues->v.x[0], 1,optional))
    764               neues->v.x[0] = 0.;
    765             if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 6, 1, double_type, &neues->v.x[1], 1,optional))
    766               neues->v.x[1] = 0.;
    767             if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 7, 1, double_type, &neues->v.x[2], 1,optional))
    768               neues->v.x[2] = 0.;
     763            if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 5, 1, double_type, &neues->v[0], 1,optional))
     764              neues->v[0] = 0.;
     765            if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 6, 1, double_type, &neues->v[1], 1,optional))
     766              neues->v[1] = 0.;
     767            if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 7, 1, double_type, &neues->v[2], 1,optional))
     768              neues->v[2] = 0.;
    769769            for (int d=0;d<NDIM;d++)
    770               neues->Trajectory.U.at(repetition).x[d] = neues->v.x[d];
     770              neues->Trajectory.U.at(repetition)[d] = neues->v[d];
    771771
    772772            // parse forces if present
    … …  
    778778              value[2] = 0.;
    779779            for (int d=0;d<NDIM;d++)
    780               neues->Trajectory.F.at(repetition).x[d] = value[d];
     780              neues->Trajectory.F.at(repetition)[d] = value[d];
    781781
    782782  //            Log() << Verbose(0) << "Parsed position of step " << (repetition) << ": (";
    … …  
    821821            neues = AtomList[i][j];
    822822          // then parse for each atom the coordinates as often as present
    823           ParseForParameter(verbose,FileBuffer, keyword, 0, 1, 1, double_type, &neues->x.x[0], repetition,critical);
    824           ParseForParameter(verbose,FileBuffer, keyword, 0, 2, 1, double_type, &neues->x.x[1], repetition,critical);
    825           ParseForParameter(verbose,FileBuffer, keyword, 0, 3, 1, double_type, &neues->x.x[2], repetition,critical);
     823          ParseForParameter(verbose,FileBuffer, keyword, 0, 1, 1, double_type, &neues->x[0], repetition,critical);
     824          ParseForParameter(verbose,FileBuffer, keyword, 0, 2, 1, double_type, &neues->x[1], repetition,critical);
     825          ParseForParameter(verbose,FileBuffer, keyword, 0, 3, 1, double_type, &neues->x[2], repetition,critical);
    826826          ParseForParameter(verbose,FileBuffer, keyword, 0, 4, 1, int_type, &neues->FixedIon, repetition,critical);
    827           if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 5, 1, double_type, &neues->v.x[0], repetition,optional))
    828             neues->v.x[0] = 0.;
    829           if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 6, 1, double_type, &neues->v.x[1], repetition,optional))
    830             neues->v.x[1] = 0.;
    831           if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 7, 1, double_type, &neues->v.x[2], repetition,optional))
    832             neues->v.x[2] = 0.;
     827          if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 5, 1, double_type, &neues->v[0], repetition,optional))
     828            neues->v[0] = 0.;
     829          if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 6, 1, double_type, &neues->v[1], repetition,optional))
     830            neues->v[1] = 0.;
     831          if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 7, 1, double_type, &neues->v[2], repetition,optional))
     832            neues->v[2] = 0.;
    833833          // here we don't care if forces are present (last in trajectories is always equal to current position)
    834834          neues->type = elementhash[i]; // find element type
    … …  
    12931293        istringstream input2(zeile);
    12941294        atom *neues = World::getInstance().createAtom();
    1295         input2 >> neues->x.x[0]; // x
    1296         input2 >> neues->x.x[1]; // y
    1297         input2 >> neues->x.x[2]; // z
     1295        input2 >> neues->x[0]; // x
     1296        input2 >> neues->x[1]; // y
     1297        input2 >> neues->x[2]; // z
    12981298        input2 >> l;
    12991299        neues->type = elementhash[No]; // find element type
    … …  
    15751575             'a'+(unsigned char)(AtomNo % 26),           /* letter for chain */
    15761576             MolNo,         /* residue sequence number */
    1577              Walker->node->x[0],                 /* position X in Angstroem */
    1578              Walker->node->x[1],                 /* position Y in Angstroem */
    1579              Walker->node->x[2],                 /* position Z in Angstroem */
     1577             Walker->node->at(0),                 /* position X in Angstroem */
     1578             Walker->node->at(1),                 /* position Y in Angstroem */
     1579             Walker->node->at(2),                 /* position Z in Angstroem */
    15801580             (double)Walker->type->Valence,         /* occupancy */
    15811581             (double)Walker->type->NoValenceOrbitals,          /* temperature factor */
    … …  
    16291629           'a'+(unsigned char)(AtomNo % 26),           /* letter for chain */
    16301630           0,         /* residue sequence number */
    1631            Walker->node->x[0],                 /* position X in Angstroem */
    1632            Walker->node->x[1],                 /* position Y in Angstroem */
    1633            Walker->node->x[2],                 /* position Z in Angstroem */
     1631           Walker->node->at(0),                 /* position X in Angstroem */
     1632           Walker->node->at(1),                 /* position Y in Angstroem */
     1633           Walker->node->at(2),                 /* position Z in Angstroem */
    16341634           (double)Walker->type->Valence,         /* occupancy */
    16351635           (double)Walker->type->NoValenceOrbitals,          /* temperature factor */
    … …  
    16831683    *output << mol->name << "\t";
    16841684    *output << 0 << "\t";
    1685     *output << Walker->node->x[0] << "\t" << Walker->node->x[1] << "\t" << Walker->node->x[2] << "\t";
    1686     *output << (double)Walker->type->Valence << "\t";
     1685    *output << Walker->node->at(0) << "\t" << Walker->node->at(1) << "\t" << Walker->node->at(2) << "\t";
     1686    *output << static_cast<double>(Walker->type->Valence) << "\t";
    16871687    *output << Walker->type->symbol << "\t";
    16881688    for (BondList::iterator runner = Walker->ListOfBonds.begin(); runner != Walker->ListOfBonds.end(); runner++)
    … …  
    17591759        *output << (*MolWalker)->name << "\t";
    17601760        *output << MolCounter+1 << "\t";
    1761         *output << Walker->node->x[0] << "\t" << Walker->node->x[1] << "\t" << Walker->node->x[2] << "\t";
     1761        *output << Walker->node->at(0) << "\t" << Walker->node->at(1) << "\t" << Walker->node->at(2) << "\t";
    17621762        *output << (double)Walker->type->Valence << "\t";
    17631763        *output << Walker->type->symbol << "\t";
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